


Reasoning

by HeyPotterhead



Series: The Story of Barnes and Simmons [2]
Category: Agents of S.H.I.E.L.D. (TV), Captain America (Movies), Marvel (Movies), Marvel Cinematic Universe, The Avengers (Marvel Movies)
Genre: All the bucky barnes tag there is, Alternate Universe, BAMF Natasha Romanov, Bucky Barnes & Steve Rogers Friendship, Bucky Barnes Feels, Bucky Barnes Has Issues, Bucky Barnes Needs a Hug, Bucky Barnes Recovering, Bucky Barnes Remembers, Bucky Barnes's Metal Arm, But she is confused, Don't hate her she deserves your love, F/M, Gen, Jemma is being mean, Memory Loss, Protective Steve, So is Bucky, Trust Issues, cold!jemma
Language: English
Status: In-Progress
Published: 2015-05-01
Updated: 2016-03-13
Packaged: 2018-03-26 16:14:49
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 4,393
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/3856963
Author URL: https://archiveofourown.org/users/HeyPotterhead/pseuds/HeyPotterhead
Summary: <blockquote class="userstuff">
              <p>
  <em>"He is volatile, dangerous, and a threat to SHIELD. He is not an asset, he is a liability.”</em>
</p><p>When Bucky Barnes was brought into the Avenger's Tower, Jemma Simmons was hell bent on helping him. But after an incident of his doing, causing one of her lab assistants to be injured, her cautious mind got the best of her and now she wasn't so sure he could be helped anymore. It all came back to a question: Was someone--something--so dangerous and unstable worth saving when everything was in already in ruins?</p><p>This is a story in which Jemma is stuck in a matter of head or heart.</p><p>(MAJOR EDIT FOR CHAPTERS 1 AND 2)</p>
            </blockquote>





	1. Chapter 1

**Notes for the Chapter:**

> Okay, first off, this chapter and the next one have some major edits. Second of all, the reason I haven't been updating this fic is because I felt like it was a hot mess; the errors and inconsistency were very significant and I feel like I should tie everything together first before I start posting again. Also, real life has been chaotic and hasn't been giving me much time to write. HOWEVER, I am on holiday now. For real. I go back to uni by the end of August (although I'll have to go there to take care of some administration stuff) but hopefully I'll be able to update as often as I hope.

“Jemma, he hates me.”

“Top of the morning to you, too,” Jemma chirped before opening the door wider to let her visitor in.

“I swear, every time I talk to him his glare just gets more and more intense? I don’t know, I feel like he’s shooting daggers through his eyes at me. It’s very unnerving,” Azalea Porter, Avengers Tower’s resident biophysicist, shuddered. She was the first friend Jemma had made since moving here along with her team. A sweet girl she was, people tend to have their prejudices towards her due to the blue hair she donned and the ink on her skin (which still made little sense to Jemma). “Stereotypes,” the American would say in a form of explanation.

“Like, seriously, from the stories Steve tells me it seemed like he was a panty dropper back in his days. Now he’s like—I don’t know—a lady ridder?” she said as she took off her lab coat and hung it on the coat rack.

Jemma laughed at her, saying, “He doesn’t hate you, Azalea. He just… Isn’t too fond of you yet—“

“—same thing—”

“—and you do realize he was brainwashed for a very long time, right?” Jemma pointed out.

“Still doesn’t change the fact that he hates me.”

“Who hates you?” Skye asked as she walked out of her room, sitting next to Azalea on the beige sofa.

“Bucky Barnes, the one and only.”

“Not surprised, though; he glares at everyone; and by everyone, I mean _everyone_ ,” Skye said. “I watched him through the two-way mirror for a few days, and if looks could kill, pretty much everyone entering the room would be dead.”

“You see my point, Jem?”

“It’s unnerving, really,” Skye said.

“That’s what I said!”

“That’s weird. He doesn’t glare at me,” Jemma said as she headed to the fridge to grab the lemon mousse cake she had been saving for lunch today.

“Well, you’re a different case. You offered him to kill you on the first day,” Azalea quipped. “I’m very sure you’re the only person he trusts in this place. Steve has made some visits, you know, trying to see where Barnes is at memory-wise. I think he’s starting to get on his good side as well.”

“That’s nice. A familiar face is good to be around in cases like these.” Jemma grabbed her bag from the kitchen counter and slung it over her shoulder.

“Also, he has a soft spot for you,” Skye said, grinning like a Cheshire cat at Jemma.

“But seriously, though. It’s like a high school-themed teen novel. He’s the handsome, brooding jock and you’re the dorky yet enchanting science geek,” Azalea said with a giggle.

“Did you just call him handsome?” Skye asked in laughter, and the blue haired girl’s face turned into a noticeable shade of red.

“Well, have you seen his jaw? It’s majestic.”

“Only you can fangirl over the killing machine downstairs,” Skye said with a sigh.

“I get my kicks where I can.”

“All right,” Jemma said, heading for the door. “It’s almost eight and I need to run some errands at the lab before I check up on our so-called ‘killing machine downstairs’. Not a fan of the nickname, I must say. Anyway, I’ll see you later.”

“Bye, Jemma,” Skye and Azalea said in unison as the door closed.

Jemma was halfway done with her errands at the lab when JARVIS informed her that May had left her an important voice message.

“Simmons, I need you at Barnes’s room _now_.” Her tone was that of someone who was nervous; rushed and unsteady. She could also hear Agent Romanov’s voice along with really loud crashing sounds. It was good cause for Jemma to be scared

Immediately she took off her gloves, grabbed a handgun from her purse and made a run for the observatory room on the forty-fifth floor. It was only three floors above, so she took the stairs. Her hands were starting to shake. She couldn’t even begin to imagine what was happening.

“What in the world happened here?” Jemma asked in astonishment the second she stepped inside the room.

It was a shipwreck; small objects and shards of glass were scattered messily all over the floor, the machines were completely destroyed and she could see blood stains on the plain white walls. In the midst of it all, James Barnes was lying on the floor; unconscious, bruised, and bleeding.

Agent Romanov and May stood near him. They looked like they put up one hell of a fight; their hair were a mess and their faces were bleeding, although not as bad as Barnes.

“Not sure but when I got here he was throwing a major tantrum. He attacked one of the lab assistants and basically smashed everything here,” May explained. “I managed to inject him with the sedative you made for him, though. So at least he’s going to be out for a while.”

Jemma was distraught by all of this. Barnes had been here for three weeks and never did he showed signs of, well, whatever just happened. He was calm and cooperative; perhaps begrudgingly, sometimes, but cooperative nonetheless. It was just strange that all of a sudden he just started breaking things and attacking people.

“Who did he attack?” Jemma asked.

“Porter; the other one. She’s with Bruce right now at the infirmary,” Romanov said. “You need to check up on Barnes, though. I think we injured him pretty bad.”

“No, I need to check up on you both first. You’re bleeding all over the place. Are you okay?”

“We can handle ourselves,” May assured. “Just go take care of Barnes.”

* * *

“Hazel,” Jemma called, walking into the infirmary.

“Hazel Porter sat on one of the hospital beds getting her forehead checked by Doctor Banner. Next to her was the older Porter, Azalea, sitting on a chair near the bed looking like she could kill somebody at the moment.

“That bastard broke my little sister’s arm! I swear if I see him I am going to—“

“Calm down, Porter,” Banner said, stitching an open wound on Hazel’s forehead. Azalea frowned, crossing her arms and muttering something Jemma couldn’t comprehend.

“What happened back there, Hazel?” Jemma asked.

“I was going to take another blood sample earlier and… I don’t know… He just started attacking me. Threw me to the wall and shit. Thank goodness Tasha and May were on the other side of the room, though. God knows what would have happened had they not been there. They beat him up pretty ba—ow!” She winced at the pain.

“Sorry,” Banner mumbled.

Jemma couldn’t seem to understand why this happened. Barnes was making progress, despite all the glaring Skye and Azalea talked about. How could he have done something so brutal? It just didn’t make sense.

She had eventually put him into another room. She made sure he was strapped this time. At first she felt guilty for doing this again to him, but when she saw Hazel looking like she took a massive beating, her guilt had easily evaporated into thin air. If it wasn’t for Romanov and May, Hazel would be pretty much dead by now. This was just the very beginning. Who knew what could happen next? Worst case scenarios began running through her head and Jemma knew that she shouldn’t have been too nice. She should have been cold and calculating since the very beginning. He was the Winter Soldier, after all. He was designed to kill; it was his true purpose.

SHIELD was already in ruins and Jemma would go to great length as to save whatever was left of it. She was definitely not going to let him ruin it. Especially since what happened at the

She knew what she had to do.

* * *

 

“Sir, I need to speak with you,” Jemma said as she barged into Coulson’s office, her heels clicking against the marble floor.

“Thank you for knocking” Coulson grinned, but it faded when he noticed the troubled look on her face. “Something wrong, Simmons?”

“Um… I’m sure you’re aware about the incident with Barnes yesterday,” she said, sitting on the chair across him. “And I would like to ask for permission, sir.”

“What for?”

“Well…” Jemma sighed, fidgeting with the hem of her sweater. _Just say it_.

“I would like to create a lethal injection for Barnes.”

Coulson froze, staring at her in surprise.

“Come again?”

“Now, I know what you’re thinking—“

“I’m thinking that you just requested permission to kill HYDRA’s main asset that would be very useful for us in taking them down,” he said.

“Yes, but—“ she struggled to find the right words. “With all due respect, sir, I thought Mr. Barnes was fine at first but I guess I was mistaken. He is volatile, dangerous and a threat to SHIELD. And to be frank, he’s more of a liability than an asset.”

“You do know we’re talking about killing a man, here, Simmons?”

“That is what comes with the job, sir, is it not?” Coulson was silent; she had a point. “He attacked Dr. Porter’s sister who is now being treated in the infirmary due to signs of a concussion. I think that’s enough reason for it. This is just for in case of emergencies; for when he becomes a threat,” she finished.

Coulson was deep in thought, trying to contemplate everything Jemma had told him. She looked at the director warily, hoping he could see what she saw.

After a long moment, he finally spoke.

“Permission denied,” he said with finality.

Jemma nodded, but anger coursed through her veins. She knew she _had_ to do it. There wasn’t really any other option.

“Thank you, sir,” she said before leaving his office.

Coulson had denied her request, but she knew somebody had to take action. And if nobody did, then it was her job to do it.

She had made up her mind.

**Notes for the Chapter:**

> Jemma, what is wrong with you?! :O Do leave me your thoughts! What did you think of the Porters, by the way? I'd like to know. Hope you enjoyed it!
> 
> River


	2. Chapter Two

She had been watching him behind a computer monitor for a week. The sedative May had given him one was one of Jemma’s earlier (and stronger,  _much_  stronger) batches; the one that was capable of knocking him out cold for an estimate of five days. On the fifth day, as he was slowly beginning to regain consciousness, however, Jemma made sure she gave him another dose, effectively putting him into another deep sleep. She wasn’t going to risk him going berserk again until she had finished creating the lethal injection.

Today wasn’t like the last seven days, though. Today she had finally finished creating what she had planned. It had taken quite a lot of Barnes's old blood samples make sure it worked on someone with the super soldier serum, but Jemma was confident the vial in her hand was going to be useful should he become a threat to anyone in the future.

A part of her felt guilty; constantly calling the other part of her a hypocrite for making him trust her, only to create a weapon against him. Perhaps for a while she did let her guard down. She became her old self again; always seeing the good in everyone. But that trait was what would kill her in times like these. Sure, she had a moment of weakness, but she wasn’t going to falter again. Not this time.

She still couldn’t decipher why he would easily trust her, though. Barnes was brainwashed and mind-controlled. He killed for sport. But he  _did_  trust her when he woke up, and that itself was already suspicious, now that she thought about it. Maybe it was his plan all along.

No, that wouldn’t make sense. Nobody knew he was going to be brought here, how would he come up with that sort of plan, anyway?

_ Maybe he worked fast? _

Jemma sighed in frustration, placing the vial on the table before burying her head in her hands. None of this makes sense. But either way, she had to take necessary precautions.

She felt responsible for the incident. Had she been more cautious then Hazel wouldn’t have gotten hurt. She was Barnes’s primary doctor, after all. He was her responsibility.

 “You’ve been here quite a lot, lately,” a voice said. Jemma snapped her head up to see none other than Bruce Banner, leaning on the door frame watching her.

Doctor Banner was one of the few people that Jemma instantly clicked with when she got here. She doesn't know him on a personal level, yet, but they talk a lot, and not just about science. Having a conversation with him was refreshing; he looked at everything with a different set of glasses. She liked his open mindedness. 

 “I tell myself the same thing,” Jemma said with a sigh. Doctor Banner smiled, walking over to her.

“So how is our brainwashed assassin?” He asked, grabbing a chair and sitting next to her.

 “He’s dormant. For now..”

 “Yeah, I can see that.” He put his glasses on and took a closer look to the monitor. “You finished with the injection yet?”

_“What?”_  Jemma was taken aback, she hasn’t told anybody about it yet—

 “You really shouldn’t tell Porter secrets. One drop of alcohol on that girl and she starts spilling.”

 “Well, I, uh... I mean—“ Jemma was at lost for words. She hadn’t really thought about how she was going to explain about her plans if anyone found out. She just planned on telling right after she gave him the shot— _i f_ it will come to that.

“You don’t have to explain anything. From personal experience, I can understand why you're doing this. On the other hand, you need to be sure that this whole thing you got going on isn't too soon,” he muttered the last part quietly. "However, you need to tell Coulson because Porter tells me you're doing this behind his back, and I can only imagine how angry he's gonna be when he finds out you've been keeping a stash of lethal injection for his current main source in taking down HYDRA under your desk." He got up from his seat and headed for the door. "Good luck, kid.”

"Oh, and Steve knows. He's super pissed, by the way," he added before leaving her alone in the room.

*          *          *

Later that day, Steve Rogers caught up with her on the way to her lab. Jemma cursed under her breath. She needed to have a conversation with Azalea very soon.

 “Simmons, please tell me that you did not create a lethal injection for Bucky?” Rogers asked as he walked next to the biochemist.

 “As a matter of fact, I have,” she simply said. There was no point in lying now. 

 “Why would you do that?”

 “Because, Barnes is dangerous.” She shrugged. “Plus, you never know when you’re going to need it. I don't understand why people are so shocked by this. It's not like I plan to kill him out of the blue. This is just to be safe.”

He stared at her in disbelief. “Wow. Fitz was right; you’re mad.”

Jemma stopped in her tracks, turning her head to look up at the blonde man towering over her in astonishment.

 “I beg your pardon?” She scoffed, her face turning red in anger. "And since when did you and  _Fitz_  started talking about me behind my back?"

 “Does it matter? This is crazy!” he yelled. “Three weeks ago you gave him a scalpel and told him to kill you if you tried to harm him. You were asking for him to  _trust_   _you_. He does, and now you made something that basically shatters that trust and would destroy our main purpose!”

"And what is that purpose, exactly, Captain Rogers?” Her voice was loud now, matching his. If he wanted a fight, he was getting a fight.

 “For him to make a full recovery!”

 “Well guess what? I don’t think that’s even probable! It was foolish of me to think otherwise. Have you seen him? He’s badly damaged. You of all people should know that there are some things you just can’t recover from,” she explained. “Besides, this injection is for emergency, just in case there comes a situation in which we need to put him down--

 “ _Put him down?_  He’s not a dog, for God’s sake!”

 “He is volatile and dangerous!” she yelled, her eyes wide and breathing rapid. Realizing how she had lost her temper--something that never happened before--she took a deep breath and tried to calm herself. Once her breathing had slowed down, she looked at Captain Rogers, whose face was grim.

There was a time when Jemma would not have done what she did; there really was. But times have changed and so do people. She was not the naive eighteen year old who just got out of the Academy and wanted to explore the world anymore. She was trying to protect what was left of SHIELD. She was done with finding answers to questions because all this time she just needed to take preventive actions.

 “I’ve realized that you need to do bad things in order to achieve the good ones. And if you can’t understand that, then I am so sorry. But I stand by my actions.” Tears had formed in her eyes, threatening to spill. But Jemma blinked them away. She didn’t like getting emotional, especially in front of someone.

He just stared at her, and she knew he was trying his best to understand where she’s coming from but she could see that he still couldn’t make sense of it. Maybe he was just too good of a person. In a world like this, she couldn’t decide if that was a good or bad thing.

 “Now if there is nothing else that you want to talk about, I should really finish my work. Good day, Captain.” 

And so she walked away quietly, letting Rogers think whatever the hell he wants to think of her. In the end it was her who was doing a favor for everyone.

 

 

**Notes for the Chapter:**

> I am sorry for the late update. I have no excuses. But I promise you'll get to see Bucky and what really happened in the next chapter.
> 
> I would also like to point out that I do not share the same views as Jemma. This is just for plot's sake!
> 
> River


	3. A Flashback

**Summary for the Chapter:**

> What really happened the day Bucky attacked Porter.

_ Seven days before _

Bucky had been held inside for three weeks. He wasn't allowed outside of the room, everyone seemed to look at him like he was filth, and staring at the walls eventually became exhausting and was slowly driving him insane. He felt like a prisoner.

Watching people in white coats walk in and out of his room made him wary, though. He didn't know why, but he became fully alert, and, astonishingly, a little bit scared every time he saw somebody in one. There was something about them that screamed _danger_ and his instincts kicked in. So he would glare; looking at them right in the eyes as a means of intimidation and warning as not to mess with him. He would glare at the mirror as well. Someone had to be watching.

The only person he didn't glare at was Doctor Simmons. Her daily visits seemed to be the least depressing thing about all this. She was nice enough. She didn't look at him the way everyone else did and out of everyone, she treated him like a normal human being for a change. She always asked him how he was doing and tried to make sure he was comfortable. She even _smiled_ at him. Perhaps it was because she dared him to kill her, or maybe it was her being the only person who actually smiles in this goddamn place, but he trusted her.

He didn't glare at Steve, too, despite having been recounted to have attempted to kill him multiple times. Steve has been making a lot of visits, just talking to him. He valued the effort, although he couldn't really talk about much anyway considering a) he remembers nothing, and b) he had attempted to kill the shield-wielding blond multiple times. Steve didn't seem to mind--he's the chirpy one in their conversations. Bucky--or so he was called--just listened.

Staying wherever the hell he was hadn't been all that exciting, and the fact that he learned how he used to be a soldier, but got taken and turned into a killing robot didn't help either. To think that he was once a normal man with parents and a little sister (all of which he was only beginning to gain vague memories about) still felt surreal. He couldn't even recall being the brainwashed assassin Steve had told him about.

Steve would tell tales about how they used to play in the park in their neighborhood every day after school, or how Bucky was always there for him when he was bullied--something Bucky still couldn't believe--and how they used to babysit Rosa, Bucky's little sister who was 17 years younger than him.

He really wish that he could laugh at all these memories because he remembers them, but sadly he couldn't. He wanted to at least be able to feel remorseful over the lives he had taken, but it was hard when he couldn't recall a single detail about it.

While he was not exactly thrilled to hear about who he was before all  _this_ , it was still an important part of him to know of it. So he let Steve talk, and he'll simply sit and listen, trying to remember something--anything.

He was beginning to remember his family, but he still couldn't remember the blond sitting beside him. Or perhaps it was just the thought that he used to be a scrawny kid that was hard to grasp.

When the day was done and the clock struck 12, Steve finally retreated to his room, leaving Bucky to his own device. It wasn't long later until he finally drifted off to slumber.

_His skin was stone cold; h_ _e could barely move. All he felt was the gentle swaying as his body was being carried by some men who he's pretty sure were from The Red Skull._

_"We brought you one of them," a voice sounded out._

_He heard a gasp, followed by footsteps making their path towards him._ _He fluttered his eyes open to discover none other than Doctor Arnim Zola._ _The man who had been experimenting on him for the whole time he was MIA._

_"Mr. Barnes! How delightful to see you again," he cheered, looking like he had just won the lottery. "I must say I never guessed I'd see you again, but this is such a wonderful surprise. And perfect timing, might I add._ _"_

_He tried to get up, tried to run. But his body was too feeble_.

 _"You see, I've been working on creating super soldiers for a long time._ _And now I have finally finished creating a serum and system that I have no doubt will work. You of all people should be proud. You will be my first successful super soldier. I can feel it."_

_"Over my dead body," he croaked._ _Zola looked at him with a dark glint in his eyes, and Bucky knew there was no chance he'd get it out of this alive._

__"We shall find out. Everyone, bring him to the table and prepare yourselves. Operation Winter Soldier will commence."_ _

__He was thrown onto a table that was just as cold as his skin. His jacket and shirt were torn away from his body and his limbs were strapped before his head was given the same treatment._ _

__Surgery lights lit up and blinded him for a while, but he could see people--doctors--all dressed in white coats and donning surgical gloves hovering over him. He set up a fight, tried to struggle, but they strapped him even harder._ _

__"Please do forgive us, Mr. Barnes. Seeing as we are in hiding, our options of medical equipments are quite... Limited, you could say. So we will have to make do with what we have."_ _

__A whirring sound was heard, and he swore his heart couldn't beat any faster. For heaven's sake, he wished someone would come through the doors and save him._ _

__"Start with the arm."_ _

__The sound was revealed to be a chainsaw, heading for his right shoulder. It finally reached his flesh and he clenched his teeth so hard, his body was shaking. The pain spread throughout his body and he felt like he was being burned and all he could do was stop himself from screaming and oh goodness he wished he was dead already._ _

__The second the saw touched his bone, he couldn't resist the pain and let out a shattering scream._ _

"Mr. Barnes? Mr. Barnes?" A gentle voice, followed by a grasp on his arm made him snap his eyes open.

 _White coat_.

He grabbed the hand that held to him and punched the woman. She fell to the floor but quickly got up, trying to escape. Bucky jumped off the bed and grabbed her by the throat, lifting her up before throwing her to the mirror, causing the glass to shatter and fall.

  
His instinct to attack overcame his senses and all he wanted to do was hurt whoever was near him. He was in a full on rage and he couldn't stop himself.

"Mr. Barnes," the woman sobbed, begging as she crawled away from him as her head bled. She held on to her right shoulder. He probably dislocated it. "Please, it's me. I--"

"What the hell did you do?"

Two women entered the room, running towards him. He tried to punch the lady with the black hair but the Redhead  got to him first and twisted his arm. He kicked her in the stomach and she fell, but Black Hair got on top of his shoulders and tried to strangle him. He ran backwards to bump her to a wall, but she held to him tighter and he was starting to lose air. Redhead tried to punch him, which he evaded by lowering his body, causing Redhead to accidentally punch Black Hair. Black hair fell to the ground and her grip on his neck was gone.

A kick to the face finally snapped him out of his daze, and suddenly White Coat became Doctor Porter, Black Hair became Agent May and Redhead became Natasha Romanov.

The anger was gone and he was suddenly overcome with guilt. He looked at Romanov, about to apologize and tell her he's back to normal, but something was stabbed to the back of his neck and his vision turned to black.

**Notes for the Chapter:**

> FINALLY AN UPDATE. If there's anyone who was actually waiting for this then I am truly sorry. First year of law school has been draining me and I just didn't have much time to write. 
> 
> I had so many doubts stopping me from updating this fic, mainly because of this irrational fear that it just wasn't good enough, but I realized that I need to put myself out there if I want to be a better writer and finally gathered the courage to post this chapter.
> 
> Anyway, what did you think about this chapter? Do send me your thoughts. They're a heck of a motivation to keep on writing and editing.


End file.
